GMOD#956 - uses bower to install jbrowse

apollo

@@ -34,6 +34,7 @@ function deploy_message(){
    echo "***************************************"
 }
 
+
 function check_node(){
     node_executable=$(which node)
     if ! [ -x "$node_executable" ] ; then
@@ -48,6 +49,17 @@ function check_node(){
     fi
 }
 
+function check_bower(){
+    bower_executable=$(which bower)
+    if ! [ -x "$bower_executable" ] ; then
+        $node_executable install -g bower
+        if ! [ -x "$bower_executable" ] ; then
+            echo "You must install 'Bower' to do a release of Apollo."
+            exit 1 ;
+        fi
+    fi
+}
+
 function check_perldependencies(){
     perl -e 'use Text::Markdown'
     if [ $? != 0 ] ; then

build.gradle

@@ -2,7 +2,10 @@
 //import java.util.zip.ZipInputStream
 //import groovy.io.FileType
 //import com.google.javascript.jscomp.*
+import org.gradle.api.tasks.Exec
+import org.apache.tools.ant.taskdefs.condition.Os
 
+//defaultTasks 'bower'
 
 /*
  * This build file was auto generated by running the Gradle 'init' task
@@ -34,6 +37,12 @@ repositories {
 }
 
 
+ext {
+    npmCommand = Os.isFamily(Os.FAMILY_WINDOWS) ? 'npm.cmd' : 'npm'
+    bowerCommand = Os.isFamily(Os.FAMILY_WINDOWS) ? 'bower.cmd' : 'bower'
+    githubURL = "https://github.com/"
+}
+
 
 ant.importBuild 'build.xml'
 
@@ -101,7 +110,7 @@ task installJBrowse(dependsOn: evaluateJBrowseConfigs) << {
     if (jbrowseConfig.git) {
         def git = jbrowseConfig.git
         if (jbrowseFile.exists()) {
-            if (git.alwaysRecheck || git.alwaysPull) {
+            if (git.alwaysRecheck || git.alwaysPull && !hasBower()) {
                 if (git.tag) {
                     fetchTags(jbrowseFile)
                     checkoutBranch(jbrowseFile, "tags/" + git.tag)
@@ -118,7 +127,7 @@ task installJBrowse(dependsOn: evaluateJBrowseConfigs) << {
             println "Cloning: ${git.url} into ${jbrowseDirectory}."
             def branch = git.branch ?: (git.tag ? "tags/${git.tag}" : null)
             cloneRepo(git.url, jbrowseDirectory, branch, 1)
-            checkoutBranch(jbrowseFile, branch)
+            if(!hasBower()) checkoutBranch(jbrowseFile, branch)
         }
     } else if (jbrowseConfig.url && !jbrowseFile.exists()) {
 
@@ -156,7 +165,6 @@ task copyApolloPlugin(dependsOn:installJBrowse,type:Copy){
     println "Copying apollo plugin"
     from("client/apollo")
     into("jbrowse-download/plugins/WebApollo")
-
 }
 
 task setupJBrowse(dependsOn: "setup-jbrowse") << {}
@@ -270,7 +278,7 @@ def cloneRepo(String url, String directory, String branch) {
     cloneRepo(url, directory, branch, null)
 }
 
-def cloneRepo(String url, String directory, String branch, Integer depth) {
+def cloneRepoNoBower(String url, String directory, String branch, Integer depth) {
     String depthString = depth != null && depth > 0 ? " --recursive --depth ${depth} " : ""
     def commandToExecute = "git clone ${depthString} ${url} ${directory} "
     println "command to execute [${commandToExecute}]"
@@ -287,6 +295,87 @@ def cloneRepo(String url, String directory, String branch, Integer depth) {
     checkoutBranch(new File(directory), branch)
 }
 
+Boolean hasBower(){
+  return true
+}
+
+task removeJBrowseDownload(type:Delete){
+    delete("jbrowse-download")
+}
+
+task moveBowerJBrowse(dependsOn:removeJBrowseDownload) {
+    doLast {
+        file("bower_components/jbrowse").renameTo(file("jbrowse-download"))
+        file("bower_components").deleteDir()
+    }
+}
+
+task installJBrowseBower(type:Exec) {
+    workingDir 'jbrowse-download'
+    commandLine './setup.sh'
+}
+
+def cloneRepoBower(String url,String directory,String branch){
+    String finalUrl = url + "#${branch}"
+    if(finalUrl.startsWith(githubURL)){
+        finalUrl = finalUrl.substring(githubURL.length())
+    }
+    exec{
+        println "using bower to install: ${finalUrl}"
+        commandLine "bower","install",finalUrl
+//        if(finalUrl.split("#")[0].endsWith("jbrowse")){
+            // mv bower_components/jbrowse -> jbrowse-download
+//        }
+        // installs it in bower_components
+    }
+
+    if(!(finalUrl.contains("#")&&finalUrl.endsWith("jbrowse"))  || finalUrl.split("#")[0].endsWith("jbrowse")) {
+        tasks.moveBowerJBrowse.execute()
+        tasks.installJBrowseBower.execute()
+    }
+}
+
+
+// Get the path for the locally installed binaries
+task npmBin << {
+    new ByteArrayOutputStream().withStream { os ->
+        exec {
+            executable = npmCommand
+            args = ['bin']
+            standardOutput = os
+        }
+        ext.binPath = os.toString().trim() + File.separator
+    }
+}
+
+
+// Install packages from package.json
+task npm(type: Exec) {
+    description = "Grab NodeJS dependencies (from package.json)"
+    commandLine = [npmCommand, "install"]
+    inputs.file "package.json"
+    outputs.dir "node_modules"
+
+    tasks.npmBin.execute()
+
+}
+
+
+// Install the bower components for front-end library management
+task bower(dependsOn: 'npm', type: Exec){
+    commandLine "${npmBin.binPath}${bowerCommand}", 'install'
+}
+
+
+def cloneRepo(String url, String directory, String branch, Integer depth) {
+    if(hasBower()){
+        cloneRepoBower(url,directory,branch)
+    }
+    else{
+        cloneRepoNoBower(url,directory,branch,depth)
+    }
+}
+
 def fetchTags(File file) {
     println "fetching tags"
     def processBuilder = new ProcessBuilder()

grails-app/conf/Config.groovy

@@ -348,8 +348,8 @@ auditLog {
 jbrowse {
     git {
         url= "https://github.com/GMOD/jbrowse"
-        tag = "1.12.1-release"
-//        branch = "master"
+//        tag = "1.12.1-release"
+        branch = "yeban-bowerise"
         alwaysPull = false
         alwaysRecheck = false
     }